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# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
import glob
class Gapfiller(Package):
"""GapFiller is a stand-alone program for closing gaps within
pre-assembled scaffolds.
Note: A manual download is required for GapFiller.
Spack will search your current directory for the download file.
Alternatively, add this file to a mirror so that Spack can find it.
For instructions on how to set up a mirror, see
http://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller"
manual_download = True
version('1.10', '54d5e2ada131a1305a66e41c0d380382')
def url_for_version(self, version):
return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
os.getcwd(),
version.dashed
)
depends_on('perl+threads', type=('build', 'run'))
def patch(self):
with working_dir('.'):
files = glob.iglob("*.pl")
for file in files:
change = FileFilter(file)
change.filter('usr/bin/perl', 'usr/bin/env perl')
change.filter('require "getopts.pl";', 'use Getopt::Std;')
change.filter('&Getopts', 'getopts')
change.filter('\r', '')
set_executable(file)
def install(self, spec, prefix):
install_tree('bowtie', prefix.bin.bowtie)
install_tree('bwa', prefix.bin.bwa)
install('GapFiller.pl', prefix.bin)
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